Thank you for your thorough reply! The 8959 appears to apply in my case because my wife and I are filing jointly, and given our combined incomes, the mistake on the university's W2 medicare wages gets added into our 8959 for additional medicare tax. That's why I was wondering if there is a way to ask the IRS for a refund for this additional 8959 medicare tax as well if I explain the error (and not just filing form 843 to ask for a refund for what is shown on the W2 that was withheld) since the W2 medicare gets fed into the 8959 and there is this extra withholding that results there. I wish the university would just issue a corrected W2 since that would fix the 8959 and avoid the 843, but at least they gave me a letter. Not sure what I can do to address the 8959 portion of the added medicare tax though and ask for a refund on that.
